2J4K

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP to 2.2 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP AND AMPPCP - HEXAMER - WITHOUT LIGANDS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK AND 2 MM UMP AND 5 MM MGCL2 MIXED WITH 2 UL MOTHER SOLUTION. MOTHER SOLUTION: 0.65 M SODIUM ACETATE, 100 MM CDCL2, 0.1 M HEPES, PH 7.5. HANGING DROP VAPOR DIFFUSION TECHNIQUE

Crystal Properties
Matthews coefficient	Solvent content
2.41	46.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.802	α = 90
b = 136.043	β = 113.17
c = 77.938	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	VERTICALLY FOCUSING CYLINDRICAL MIRROR	2005-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711		MAX II	I711

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	22.54	99.3	0.11	12	3.4		72006		-3	22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	98.7		0.65	2.3	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP AND AMPPCP - HEXAMER - WITHOUT LIGANDS	2.2	21.67	71829	3363	99	0.219	0.219	0.251	RANDOM	35.6

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.26		6.14	-1.31		0.05

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22
c_scangle_it	3.05
c_mcangle_it	2.38
c_scbond_it	2.06
c_mcbond_it	1.43
c_angle_deg	1.2
c_improper_angle_d	0.79
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10009
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	145

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing